Related papers: Suffix Arrays for Spaced-SNP Databases
Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
Suffix Array (SA) is a cardinal data structure in many pattern matching applications, including data compression, plagiarism detection and sequence alignment. However, as the volumes of data increase abruptly, the construction of SA is not…
Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…
Biological data mainly comprises of Deoxyribonucleic acid (DNA) and protein sequences. These are the biomolecules which are present in all cells of human beings. Due to the self-replicating property of DNA, it is a key constitute of genetic…
Motivation: Researchers need a rich trove of genomic datasets that they can leverage to gain a better understanding of the genetic basis of the human genome and identify associations between phenotypes and specific parts of DNA. However,…
A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique which we call accelerated sampling. It runs in optimal O(n/p) local computation and communication, and requires a near…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…
We present simplicial neural networks (SNNs), a generalization of graph neural networks to data that live on a class of topological spaces called simplicial complexes. These are natural multi-dimensional extensions of graphs that encode not…
Single nucleotide polymorphisms (SNPs) are variations at specific locations in DNA. Sequence responsible for marking genes associated with diseases or tracking inherited diseases within The family. These variations in the Rb1 gene can cause…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Recently, different works proposed a new way to mine patterns in databases with pathological size. For example, experiments in genome biology usually provide databases with thousands of attributes (genes) but only tens of objects…
DNA fingerprinting is a cornerstone for human identification in forensics, where the sequence of highly polymorphic short tandem repeats (STRs) from an individual is compared against a DNA database. This presents significant privacy risks…
Morphisms are homomorphisms under the concatenation operation of the set of words over a finite set. Changing the elements of the finite set does not essentially change the morphism. We propose a way to select a unique representing member…
The multidimensional databases often use compression techniques in order to decrease the size of the database. This paper introduces a new method called difference sequence compression. Under some conditions, this new technique is able to…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
The usefulness of a `total-evidence' approach to human population genetics was assessed through a clustering analysis of combined genome-wide SNP datasets. The combination contained only 3146 SNPs. Detailed examination of the results…